Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Marie-Hélène Bourget¹, Lee Kamentsky², Satrajit S Ghosh^{3

4}, Giacomo Mazzamuto^{5

6}, Alberto Lazari⁷, Christopher J Markiewicz⁸, Robert Oostenveld^{9

10}, Guiomar Niso¹¹, Yaroslav O Halchenko¹², Ilona Lipp¹³, Sylvain Takerkart¹⁴, Paule-Joanne Toussaint¹⁵, Ali R Khan¹⁶, Gustav Nilsonne^{17

18}, Filippo Maria Castelli⁶; BIDS Maintainers; Julien Cohen-Adad^{1

19

20}

Collaborators, Affiliations

Collaborators

BIDS Maintainers:
Stefan Appelhoff, Ross Blair, Eric Earl, Franklin Feingold, Anthony Galassi, Rémi Gau, Christopher J Markiewicz, Taylor Salo

Affiliations

¹ NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada.
² Kwanghun Chung Lab, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, United States.
³ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States.
⁴ Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, United States.
⁵ National Research Council, National Institute of Optics, Sesto Fiorentino, Italy.
⁶ European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy.
⁷ Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, Oxford, United Kingdom.
⁸ Department of Psychology, Stanford University, Stanford, CA, United States.
⁹ Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.
¹⁰ NatMEG, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
¹¹ Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States.
¹² Department of Psychological and Brain Sciences, Center for Open Neuroscience, Dartmouth College, Hanover, NH, United States.
¹³ Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
¹⁴ Institut de Neurosciences de la Timone, CNRS-Aix Marseille Université, Marseille, France.
¹⁵ Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
¹⁶ Robarts Research Institute, University of Western Ontario, London, ON, Canada.
¹⁷ Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
¹⁸ Swedish National Data Service, Gothenburg University, Gothenburg, Sweden.
¹⁹ Mila - Quebec AI Institute, Montreal, QC, Canada.
²⁰ Functional Neuroimaging Unit, Centre de Recherche de l'Institut Universitaire de Montréal (CRIUGM), Université de Montréal, Montreal, QC, Canada.

PMID: 35516811
PMCID: PMC9063519
DOI: 10.3389/fnins.2022.871228

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Marie-Hélène Bourget et al. Front Neurosci. 2022.

. 2022 Apr 19:16:871228.

doi: 10.3389/fnins.2022.871228. eCollection 2022.

Authors

Collaborators

BIDS Maintainers:
Stefan Appelhoff, Ross Blair, Eric Earl, Franklin Feingold, Anthony Galassi, Rémi Gau, Christopher J Markiewicz, Taylor Salo

Affiliations

¹ NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada.
² Kwanghun Chung Lab, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, United States.
³ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States.
⁴ Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, United States.
⁵ National Research Council, National Institute of Optics, Sesto Fiorentino, Italy.
⁶ European Laboratory for Non-Linear Spectroscopy (LENS), Sesto Fiorentino, Italy.
⁷ Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, Oxford, United Kingdom.
⁸ Department of Psychology, Stanford University, Stanford, CA, United States.
⁹ Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.
¹⁰ NatMEG, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
¹¹ Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States.
¹² Department of Psychological and Brain Sciences, Center for Open Neuroscience, Dartmouth College, Hanover, NH, United States.
¹³ Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
¹⁴ Institut de Neurosciences de la Timone, CNRS-Aix Marseille Université, Marseille, France.
¹⁵ Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
¹⁶ Robarts Research Institute, University of Western Ontario, London, ON, Canada.
¹⁷ Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
¹⁸ Swedish National Data Service, Gothenburg University, Gothenburg, Sweden.
¹⁹ Mila - Quebec AI Institute, Montreal, QC, Canada.
²⁰ Functional Neuroimaging Unit, Centre de Recherche de l'Institut Universitaire de Montréal (CRIUGM), Université de Montréal, Montreal, QC, Canada.

PMID: 35516811
PMCID: PMC9063519
DOI: 10.3389/fnins.2022.871228

Abstract

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.

Keywords: data sharing; data structure; microscopy; open science; specification; standardization.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

**FIGURE 1**
Microscopy-BIDS overview. **(A)** Microscopy-BIDS dataset hierarchy. The raw imaging data files and their sidecar JSON files are stored in the “sub- < *label* >” directory, followed by the optional “ses- < *label* >” (session) directory and then the data type “micr” directory. The new “sample- < *label* >”, “chunk- < *label* >”, and “stain- < *label* >” entities are shown in red in the image filename. **(B)** Example of “samples.tsv” file describing sample attributes such as “sample_type”. **(C)** Example of “participants.tsv” file including animal metadata (“species”, “strain”, and “strain_rrid”). **(D)** Example of sidecar JSON metadata file. **(E)** Raw microscopy imaging data modified from Zaimi et al. (2018) under Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).

**FIGURE 2**
Examples of chunk configurations. **(A)** Ordered 2D chunks without overlap. **(B)** Ordered 2D chunks with overlap. **(C)** Unordered 2D chunks with and without overlap. **(D,E)** Ordered 2D chunks on different 3D planes. **(F)** Ordered 3D chunks.

See this image and copyright information in PMC

References

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Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Collaborators

Affiliations

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

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